"We believe in attacking US and its allies but we are not involved in this attack," Tehreek-e-Taliban Pakistan (TTP) spokesman Ehsanullah Ehsan told AFP.
"We have no connection to this bombing but we will continue to target them wherever possible," Ehsan added.
Monday's explosions at the Boston Marathon, one of America's top sporting events, forced cities from New York to Los Angeles to go on high alert and conjured up memories of the September 11, 2001 attacks.
The Pakistani government said the country was "deeply shocked and saddened" by the Boston attack.
"The government of Pakistan condemns this heinous act of terrorism in the strongest possible terms and hopes that the perpetrators of this barbaric act will be brought to justice," said a statement issued by the foreign ministry.
An Internet video purportedly from the TTP claimed responsibility for a car bomb attempt in New York's Times Square on May 1, 2010, for which Pakistani-American Faisal Shahzad was jailed for life.
A TTP spokesman later denied that the faction had trained or recruited Shahzad.
Shahzad said during his trial that he received bomb-making training during a 40-day stay with the Pakistani Taliban, but that on his return to the United States he planned the bombing and acted alone.
He was also shown in a video embracing Hakimullah Mehsud, commander of the TTP, who has vowed to attack major US cities.
The TTP is based in Pakistan's northwestern tribal belt on the Afghan border and has been blamed for some of the deadliest suicide attacks in Pakistan.
US President Barack Obama warned against "jumping to conclusions" but a senior White House official, speaking on condition of anonymity, said such an attack was "clearly an act of terror".